High level and stable recombinant protein (r-protein) production in mammalian cells is important for cost-effective biotherapeutic manufacturing. S/MARs (Scaffold/Matrix Attachment Regions) are 70% AT-rich sequences, which are believed to play many important roles in chromatin function. In addition to their structural function, S/MARs play important roles in temporal and spatial organization of gene expression (Alvarez 2000; Liu 1997). The inclusion of an S/MAR sequence in an expression vector can thus help increase the level of expression and prevent silencing of the transgene (Phi-Van 1990; Jenke 2004; Zahn-Zabal 2001; Kim 2004). MAR elements have been shown to work either after integration into the host genome or as part of episomal vectors (Halweg 2005; Girod 2005).
Genomic elements such as UCOE (from Millipore) or MAR (from Selexis) are available and have proven to enhance expression level and stability when provided in cis or in trans in expression vectors used to generate stable cell lines. There are many S/MARs in the human genome that can be incorporated into expression vectors for enhancing productivity and stability of clonal cell lines (Girod 2007). However, not all of these sequences show beneficial effects (Sass 2005) and these sequences are very often very large (1.5 to 4 kb) and as such not practical to incorporate in expression vectors. There is a need to identify S/MAR sequences that are short (<1 kb) while still efficient, but the only way to achieve this is through a trial-and-error approach.